PROSITE documentation PDOC00028
Zinc finger C2H2-type domain signature and profile


'Zinc finger' domains [1,2,3,4,5] are nucleic acid-binding protein structures first identified in the Xenopus transcription factor TFIIIA. These domains have since been found in numerous nucleic acid-binding proteins. A zinc finger domain is composed of 25 to 30 amino-acid residues. There are two cysteine or histidine residues at both extremities of the domain, which are involved in the tetrahedral coordination of a zinc atom. It has been proposed that such a domain interacts with about five nucleotides. A schematic representation of a zinc finger domain is shown below:

                                 x  x
                               x      x
                              x        x
                              x        x
                              x        x
                              x        x
                               C      H
                             x   \  /   x
                            x     Zn     x
                             x  /    \  x
                               C      H
                      x x x x x        x x x x x

Many classes of zinc fingers are characterized according to the number and positions of the histidine and cysteine residues involved in the zinc atom coordination. In the first class to be characterized, called C2H2, the first pair of zinc coordinating residues are cysteines, while the second pair are histidines. A number of experimental reports have demonstrated the zinc-dependent DNA or RNA binding property of some members of this class.

Some of the proteins known to include C2H2-type zinc fingers are listed below. We have indicated, between brackets, the number of zinc finger regions found in each of these proteins; a '+' symbol indicates that only partial sequence data is available and that additional finger domains may be present.

  • Saccharomyces cerevisiae: ACE2 (3), ADR1 (2), AZF1 (4), FZF1 (5), MIG1 (2), MSN2 (2), MSN4 (2), RGM1 (2), RIM1 (3), RME1 (3), SFP1 (2), SSL1 (1), STP1 (3), SWI5 (3), VAC1 (1) and ZMS1 (2).
  • Emericella nidulans: brlA (2), creA (2).
  • Drosophila: AEF-1 (4), Cf2 (7), ci-D (5), Disconnected (2), Escargot (5), Glass (5), Hunchback (6), Kruppel (5), Kruppel-H (4+), Odd-skipped (4), Odd-paired (4), Pep (3), Snail (5), Spalt-major (7), Serependity locus β (6), delta (7), h-1 (8), Suppressor of hairy wing su(Hw) (12), Suppressor of variegation suvar(3)7 (5), Teashirt (3) and Tramtrack (2).
  • Xenopus: transcription factor TFIIIA (9), p43 from RNP particle (9), Xfin (37 !!), Xsna (5), gastrula XlcGF5.1 to XlcGF71.1 (from 4+ to 11+), Oocyte XlcOF2 to XlcOF22 (from 7 to 12).
  • Mammalian: basonuclin (6), BCL-6/LAZ-3 (6), erythroid krueppel-like transcription factor (3), transcription factors Sp1 (3), Sp2 (3), Sp3 (3) and Sp(4) 3, transcriptional repressor YY1 (4), Wilms' tumor protein (4), EGR1/Krox24 (3), EGR2/Krox20 (3), EGR3/Pilot (3), EGR4/AT133 (4), Evi-1 (10), GLI1 (5), GLI2 (4+), GLI3 (3+), HIV-EP1/ZNF40 (4), HIV-EP2 (2), KR1 (9+), KR2 (9), KR3 (15+), KR4 (14+), KR5 (11+), HF.12 (6+), REX-1 (4), ZfX (13), ZfY (13), Zfp-35 (18), ZNF7 (15), ZNF8 (7), ZNF35 (10), ZNF42/MZF-1 (13), ZNF43 (22), ZNF46/Kup (2), ZNF76 (7), ZNF91 (36), ZNF133 (3).

In addition to the conserved zinc ligand residues it has been shown [6] that a number of other positions are also important for the structural integrity of the C2H2 zinc fingers. The best conserved position is found four residues after the second cysteine; it is generally an aromatic or aliphatic residue. A profile was also developed that spans the whole domain.


In proteins that include many copies of the C2H2 zinc finger domain, incomplete or degenerate copies of the domain are frequently found. The former are generally found at the extremity of the zinc finger region(s); the latter have typically lost one or more of the zinc-coordinating residues or are interrupted by insertions or deletions. Our pattern does not detect any of these finger domains.

Expert(s) to contact by email:

Becker K.G.

Last update:

May 2004 / Text revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

ZINC_FINGER_C2H2_2, PS50157; Zinc finger C2H2 type domain profile  (MATRIX)

ZINC_FINGER_C2H2_1, PS00028; Zinc finger C2H2 type domain signature  (PATTERN)


1AuthorsKlug A. Rhodes D.
SourceTrends Biochem. Sci. 12:464-469(1987).

2AuthorsEvans R.M. Hollenberg S.M.
TitleZinc fingers: gilt by association.
SourceCell 52:1-3(1988).
PubMed ID3125980

3AuthorsPayre F. Vincent A.
TitleFinger proteins and DNA-specific recognition: distinct patterns of conserved amino acids suggest different evolutionary modes.
SourceFEBS Lett. 234:245-250(1988).
PubMed ID3292287

4AuthorsMiller J. McLachlan A.D. Klug A.
TitleRepetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes.
SourceEMBO J. 4:1609-1614(1985).
PubMed ID4040853

5AuthorsBerg J.M.
TitleProposed structure for the zinc-binding domains from transcription factor IIIA and related proteins.
SourceProc. Natl. Acad. Sci. U.S.A. 85:99-102(1988).
PubMed ID3124104

6AuthorsRosenfeld R. Margalit H.
TitleZinc fingers: conserved properties that can distinguish between spurious and actual DNA-binding motifs.
SourceJ. Biomol. Struct. Dyn. 11:557-570(1993).
PubMed ID8129873

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